Tuesday, December 17, 2013

Exam questions for 2nd year students in a critical thinking course

Here are the questions on yesterday's exam for students in my course. Students will be graded on their explanations and not so much on the actual answer they give. The idea is to reward critical thinking and that includes the ability to see both sides of an issue and recognize problems with whatever side you choose to defend.

Assuming that the technology is safe and effective, should we, or should we not, have laws forbidding the cloning of humans?

What is the best definition of a "gene"? Explain why you choose that definition and give examples of possible "genes" that don’t fit your definition.

Elliott Sober is a highly respected philosopher. He explains that theistic evolution is a reasonable hypothesis because God could easily cause mutations to occur in a way that scientists would not be able to detect. In other words, a specific, directed, mutation would be indistinguishable from a random mutation. Thus, it would appear that evolution was an entirely naturalistic process while, in fact, its direction was being guided by God. Do you think this is a reasonable argument in support of theistic evolution? Why or why not?

In his book, The Myth of Junk DNA, Jonathan Wells writes.

According to intelligent design (ID), it is possible to infer from evidence in nature that some features of the world, and of living things, are better explained by an intelligent cause than by unguided natural processes.

What sorts of positive arguments do ID proponents use to support this inference from evidence in nature? Are they effective?

37 comments
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1. By conceding the premise "safe and effective" (which I assume means (among other things) it produces otherwise healthy viable "normal" people every time it is attempted), this is purely a public policy question on whether we should permit asexual human reproduction. Since I don't find the question interesting, I'm going to skip this one. :-)

2. I like Dawkins' definition from the Selfish Gene: "any portion of chromosomal material that potentially lasts for enough generations to serve as a unit of natural selection". This in an inclusive definition, and so really potentially any part of the genome could be considered a gene if it affects the phenotype (and merely existing as something the organism needs to expend energy to duplicate possibly does it). Thus, the protein coding regions of the chromosome would each be a separate gene, but so would, for example, each of the many promoter regions that exist. What this definition is not good at is defining physical the limits of a gene, and so it is not a good definition for some purposes.

3. The theory that Sober's argument aims to support is not falsifiable, so therefore his argument is not useful in helping discover anything. (If it God's influence truly is not discernable, then it is superfluous.)

4. ID essentially boils down to "god of the gaps". Unfortunately in many cases the "gap" is really a "gap" in the understanding of the ID'er, not in the understanding of those most knowledgeable on the topic. A typical argument is "I don't understand this, and based on this evidence [quote mines, misrepresentations, confused understanding, and sometimes outright deception and lies] it appears the experts don't either, so therefore the Christian God." They are not effective arguments because of this major flaw.

4. They have put forward Irreducible complexity, but irreducible complexity doesn't mean design. For instance, in the case of the bacterial flagellum, scientists found that it evolved via gene duplication, divergence and co-option. They also claim that CSI (low probability associated with a pattern) means that something is design. However, no one demonstrated that and the only thing to which some form of calculation was applied was the bacterial flagellum. But the bacterial flagellum evolved.

One more thing about question 4: They also said that was no Junk in the genome and that that was a prediction of I.D. But natural selection could also account for that. Meanwhile, there's plenty of DNA that does nothing important in our genome - it's junk. An example: ERV and transposons.

About question 2: A gene can be defined as a stretch DNA that are capable of producing a polypeptide or an RNA chain that has a function in the organism. I've choosen this definition because it is somehow restrictive - for instance, transposons are mostly junk, so they don't fit this defenition. Pseudo-genes do not fit this discription too, nor truncated genes.

I guess like many definitions, including the def of life itself, things get a little cumbersome and full of caveats and qualifications. Perhaps an even better example than polycistronic operons (where I would consider lacZYA to be separate genes) is how some polypeptides (e.g in some viruses) are proteolytically processed to form several independent proteins. I guess I would still call that one gene encoding the full polypeptide but obviously that would obscure functionally important downstream details.

«Are introns part of your definition?» As the term intron refers to both DNA and RNA sequences, I think the DNA sequence (of the intron) would fit the definition, but only that one which refers to the splicing region, because it is the only one that has a function. But the whole intronic region wouldn't fit, because not all of it is important to the organism.

«How many "genes" in the lac operon and how does this follow from your definition?» Four genes (one regulator and three structural genes that code for enzymes). They all code for proteins that have an important function, so that fits my definition.

About question 3: I think it's a matter of parsimony: I think the basic mechanisms of evolution (random mutation, random genetic drift and natural selection) work just fine to account for what we observe in living things and if the same mechanisms + god also work fine, so the most parsimonious hypothesis will be the first (the no god hypothesis) and that would be chosen insted of the other. God is also superfluous and also doesn't help us explaining anything.

About question 3 (I know - here we go again): It's not even an argument that supports theistic evolution, but an argument that supports the idea that evolution is compatible with a god that intervenes in the biological world and intervened in our origins. But still, in terms of parsimony, the hypothesis that god intervenes in such way is not the perferred one.

Just one more thing: not al "theistis evolutionists" think that this is what happens - some of them think god somehow originated the universe and that evolution occurred all by itself, but that it was part of god's plan. It's still weird. This belief all by itself doesn't illustrates theism, it illustrates deism, but many people who believe it also believe that god can and does intervenes in human affairs and (now it gets weirder) somehow introduced a soul on humans.

For four.No biology is explained beyond trivial speciation, if that, by evolution.So all biology is explained by original creation and then independent mechanisms within the biology to preserve the biology existence. this because of the fall and death.Its excellent evidence in looking at the complexity of biology and looking closely at its most reducible elements and still finding so complex as to be impossible from bumping natural causes.Its about complexity not being reducible. Thats the evidence for a creator on these points.questioning this reasoning and why IS where critical thinking should kick in.isn't critical thinking just accurate thinking based on data and then complaints the other guy isn't doing it?

By the way I note heavy criticism of creationism here. thats fine with me and welcome to see this in university classes BUT , here it comes, whats good for the goose is good for the gander !Creationists must also be allowed in classes to do likewise and not be fired for bring in religion in science .If one can attack ID./YEC then one can assert ID/YES or attack the criticisms.i got a hunch execution at dawn would be the result for the creationist or any intellectual/establishment rebel!

i got a hunch execution at dawn would be the result for the creationist or any intellectual/establishment rebel!

Your hunch certainly isn't based on the historical norm then, is it? Robert you seem to be, after a fashion, a thoughtful person. How can you place so much stock in human interpretations of an obviously man-made text that is based on thoughts, ancient beliefs, and suspect revelations? Every ounce of your reasoning is based upon the expected inerrancy of an ancient text. Surely you must see a problem with this.

Thoughtful people must conclude its a option the bible is true. Its not settled its false. Thats just what some human beings say.Yes I'm confident the bible is the truth.

Anyways, largely, reasonings are unrelated to scripture.its only a foundation confidence.One simply has examined evolution and simply attacks it on its lack of merit.Only a minority of our criticisms are based on biblical presumptions.its mostly on the wrong and scientifically careless ides of evolutionary biology.

1. Unless some excertionally good reasons for cloning can be given (and I can't think of any, we already need a couple more Earths to support the current population), cloning should be prohibited.

2. Without consulting sources, the (a) gene is the basic unit (collection of base pairs) of 'productive' code in DNA. Pseudogenes do not fit my concept of productive genes. But the presence of a productive gene doesn't imply that it is always active and performing a function. It is obvious, any cell will have the genes it needs to perform its duty active and the rest will be sleeping. or something like that.

3. There are many reasons why theistic evolution looks like a very convoluted attempt at reconciliation of religious faith with science. Ockhams razor tells me that a God worth his salt doesn't resort to magic to make the world he created run. Assuming unlimited powers, why would he bother when he, already being omniscient already knew that a big bang would let him off the hook, so to speak - without being burdened with running the show he had set in motion.

4. False application of logic. Watches are made, therefore biology is made. No mention of the fact that there is a fundamental difference between mechanical devices that we know are manufactured; that are stone dead and never will replicate - and the world of biology which rely on replication, and contain the features required for survival and reproduction.

No, their arguments are not effective, they are impotent and explain nothing. And yet they have the desired effect, people with a desire to defend religious faith have found a way out of the obvious problem of defending belief in a mere 6000 years old earth against the overwhelming evidence that it is billions of years old. Takes a lot of wishful thinking to deny that, so they have found a convenient god-of-the gaps so they can brush evidence they don't like under the carpet. It is however interesting to note that hiding the identity of the 'designer' to make ID look scientific has mot worked, it seems most supporters of ID says God is the "designer". How, where and when the designs are implemented has never been revealed. I suppose it would be embarassing to admit it could only be done with magic.

Wow - not only are identical twins impossible, but when they nevertheless appear there is an issue with their consciousness? Why would a human have a consciousness issue (whatever that means) just because someone else has the same DNA?

Concerning question no. 1:First I would ask whether you really mean the legal question (should cloning be outlawed?) or the ethical one (is it morally right to clone somebody/oneself?) since these are separate question the former one being more complicated and including the latter.

Assuming the legal question is really the question you meant I have to ask if safety and effectiveness are really the right and only criteria. In most parts of Europe for example you are not allowed to carry fire arms despite the fact that fire arms are effective (though maybe you could get into an argument what you actually mean by effective) and safe (safe for the person using it by reasonable standards). So apparently there are other criteria at play to determine whether something should be legal or not.

Since you said recently on this blog that you don't know what bioethics are I will add this: One reason why you would ban things like cloning or assisted suicide is that you want to protect people and the society from harm. This is analogue to the arguments why drugs should be illegal. It is argued that people can't responsibly take drugs without causing disproportionate harm to themselves and/or society. This is an utilitarian way of looking at things that is quite difficult to argue because you have to weight the benefits against the harm.(Since you gonna ask what the possible harm could be in these things I will give you examples: In the case of assisted suicide you could argue that that may lead society into pressuring terminally ill people to commit suicide to save money so a ban would contribute to the protection of the people. In the case of cloning you could argue that somebody rich could clone himself millions of times thus skewing the genetic pool or causing overpopulation. I'm not saying that these arguments are good I'm just saying that these could be made.) So bioethics deals with ethical questions that are related to medicine, broadly speaking.

Beneath the legal on the purely ethical level you would need to make value judgments. One point of view you could take is that humans are not allowed to interfere with the natural order, as on example. This position can't be argued with in one sense because it is a value judgment. The only thing that you can do is to ask whether this position is really a consistent one considering other possible violations of the natural order.

On the other side one position would be that bodily autonomy is a value of highest importance, the greatest good, thus cloning must be legal. This arguments is frequently made in the context of legal abortion and thus a fair warning is necessary in my opinion. If you take this position you really don't have any avenue left to argue against legalizing pornography, doping, prostitution, drugs etc. This is a powerful moral value to advocate for and a deeply consequential one.

First I would ask whether you really mean the legal question (should cloning be outlawed?) or the ethical one (is it morally right to clone somebody/oneself?) since these are separate question the former one being more complicated and including the latter.

They are not separate questions. My students know full well that the main reason we have laws against cloning is that politicians are sensitive to "ethical" beliefs.

I have to ask if safety and effectiveness are really the right and only criteria.

Nope. They aren't. You don't get any marks for stating the obvious.

One reason why you would ban things like cloning or assisted suicide is that you want to protect people and the society from harm.

Yes, that's one possible argument. It's not a very good one, but it's possible ... as you say.

So bioethics deals with ethical questions that are related to medicine, broadly speaking.

You just gave an example of a perfectly good cost-benefit debate. What has that got to do with ethics?

One point of view you could take is that humans are not allowed to interfere with the natural order, ...

That's one of the main reasons given for the Canadian ban on human cloning. I expect my students will discuss whether this is a good argument or not. The issue is whether your "value judgement" should be imposed on others.

If you take this position you really don't have any avenue left to argue against legalizing pornography, doping, prostitution, drugs etc.

"You just gave an example of a perfectly good cost-benefit debate. What has that got to do with ethics?"

These are not the only things to consider. With cloning you have the same ethical question as with abortion: When do you grant the thing human rights.

The feminist say: as long as it is inside the womb 0 % rights outside the womb 100 % rights. While you can argue about that that is at least a rather defined point.

So what about the clone? Does the clone ever attain human rights? Is the clone a slave? I assume the clone at least at first is the property of the donor but does the clone ever cease to be property? If yes, when? If not, why should "normal" children attain human rights and not stay the property of their parents?

If you define ethics as just being about cost-benefits calculations when this is just one possible definition.

Why should he/she be a slave? Are traditionally conceived children slaves? Aren't "identical" twins independent individuals with separate identities and personalities? A clone is not a xerox copy of the donor, whatever people imagine.

I assume the clone at least at first is the property of the donor but does the clone ever cease to be property? If yes, when? If not, why should "normal" children attain human rights and not stay the property of their parents?

I fail to see why a clone should have a status different from that of any other human being. What's supposed to be so special about clones from the ethical or legal point of view?

A few decades ago it was against the natural order for women to wear trousers. I suppos etaking antibiotics is an unnatural way of fighting bacterial infections, and blogging on the Internet is an unnatural form of communication. Throughout our history as an intelligent species we have enthusiastically interfered with the natural order. It all started with making tools, using fire, and building artificial shelters.

Given that no one has promoted any arguments for why humans with near-identical DNA should be considered an ethical question at all (and that none of those I personally know consider their own existence to be an ethical question), let's switch to another part of 2nd op's bizarre argument:

Guns are banned in countries that value public safety precisely because they are _not_ safe - most importantly, if person A is allowed the means of firing a bullet through person B's head, person B is not safe. So here we have a law that was clearly made to enhance safety being used to (somehow) make the completely obvious and superfluous point that safety is not be the only consideration. The mind boggles.

C.J.Cherryh's "Cyteen" novels depict a future society which uses cloning and psychological techniques to reproduce geniuses (not just genetically identical but raised with similar stimuli with the intent of reproducing the same sort of person with the same interests and drives).

The main reason this is done is to continue the research which the genius started in her first lifetime. However, there is also a dynastic element, since in this (unlikely) future interstellar society (one of several that coexist in Cherryh's novels), scientists happen to have a lot of political power.

I think I would consider having an Einstein or two always on hand as beneficial to society. However, it is more likely that we would wind up having several Donald Trumps.

There are several other science-fiction stories which consider cloning to be one of those things which, if it can happen, will happen, and perhaps I have been conditioned by them, but I guess my position would be not to deny cloning to those want it and can afford it - with the same obligations to the clone as parents have to their children.

I am not sure how we get from here to there, though. The necessary trial-and-error (evolutionary) research to perfect human cloning might involve severe risks to the first clones. I would be happier letting random genetic variation continue to give us our geniuses.

The arguments proponents of ID use focus on the relationship between human design and design in nature. More specifically, they argue that some features of nature could only have been caused by an intelligence. A generalised form of the argument could be stated as follows:1. There are certain features of design that are only possible with intelligent agency2. In nature, there are certain features that satisfy (1).3. Therefore, it is reasonable to infer that an intelligent agency is the cause of those features.Michael Behe's proposal of Irreducible Complexity (IC) is an example of the satisfaction of (1). An IC system is one where several parts all contribute to the basic function of the system such that the removal of any one part would leave the system non-functioning. This claim rests on being able to demonstrate that such systems cannot come about without intelligence.

Another formalised argument is William Dembski's explanatory filter. The filter first asks if chance or regularity are sufficient to account for the probability of the phenomenon, and if not, then design is inferred. As Dembski argues, this could mean false negatives (where that which ultimately could be explained by chance or law fall through to design), but what he argues is that the inference should demonstrate design, as he does by applying it to cases where it applies for human design.

So there are two main strategies that could make design a more reasonable hypothesis.1. intelligent design is the only known way to get certain features2. intelligent design is a more likely hypothesis for certain features

There are problems with the arguments, however, that cast doubt on just how effective these arguments are.

To demonstrate that a process cannot happen with current evolutionary theory runs the risk of making the argument from ignorance, as anyone in the 18th century would have done in the absence of knowledge of the insights Darwin brought to the process. Behe's IC systems might have been something that couldn't evolve with present mechanisms, but the inference would still be in the absence of knowledge of how it happened. Behe's argument turned out to be conceptually wrong, as demonstrated with Muller's two-step process for interlocking complexity, so the inference to design is not the only path to IC systems.

The inference to design adds a new element to the system, a new designer. With human design, we have agents capable of doing the design, and inferences to human design require a sober assessment of our abilities. Before intelligent life evolved on this planet, however, there is no known designer that can be appealed to. The designer(s) would be something new to account for, and something grand at that. If we came across an an artefact on an uninhabited island, we would infer that humans had once lived there. If we came across it in the Cambrian rocks, we'd have no obvious candidate for who would have made it and how it ended up there.

There is a way of making unknown designer(s) a more likely hypothesis than natural processes that echoes David Hume's sentiments on miracles. We could epistemologically treat the inference to design in the same way Hume treated the proposition that a miracle occurred, as the designer itself is intervening against the naturalistic background. Since we have experience of the natural processes being as they are, and don't have experience of external designers, the inference to design would require a sufficiently low probability of natural processes accounting for the particular observation in question. This would require knowing present theory is a correct account of biological processes, and that this account would be insufficient. Design would be the more likely hypothesis if the implausibility of it happened naturally would exceed the implausibility of an unknown designer intervening. At present, this challenge has not been satisfied by ID proponents.

My (old, oft-stated) argument against "Intelligent Design" is that to have validity it must explain why "intelligence" and "design" are necessary to explain things seen in nature, but to do that it must understand how intelligence and design work, and the IDers show no grasp of either. For example, suppose both intelligence (the working of brains and nervous systems) and design (the working of design engineers such as myself) work by using evolutionary algorithms, such as trial and error (which I believe based on my experience and reading to be the case). Then there is no conflict, no magic, separating the works of man from the Theory of Evolution, and every argument the IDer's made against the possibility of evolutionary methods working would rebound against them. The arguments themselves are unsound, of course, but it seems absurd to have a counter-theory based on concepts which are not themselves well-understood. "Creation by Magic" might be a more appropriate name which better conveys the scientific content of "Intelligence Design".

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.